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- EMDB-15686: Cryo-EM structure of DrBphP in Pfr state -

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Basic information

Entry
Database: EMDB / ID: EMD-15686
TitleCryo-EM structure of DrBphP in Pfr state
Map data
Sample
  • Complex: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
    • Protein or peptide: Bacteriophytochrome,Response regulator
  • Ligand: BILIVERDINE IX ALPHA
Function / homology
Function and homology information


osmosensory signaling via phosphorelay pathway / detection of visible light / phosphorelay response regulator activity / protein kinase activator activity / histidine kinase / phosphorelay sensor kinase activity / photoreceptor activity / phosphorelay signal transduction system / regulation of DNA-templated transcription / ATP binding / identical protein binding
Similarity search - Function
Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain ...Phytochrome, PHY domain superfamily / PAS fold-2 / PAS fold / Phytochrome, central region / Phytochrome region / Phytochrome chromophore attachment domain / Phytochrome chromophore attachment site domain profile. / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Response regulator receiver domain / cheY-homologous receiver domain / Signal transduction response regulator, receiver domain / Response regulatory domain profile. / GAF domain / CheY-like superfamily / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily
Similarity search - Domain/homology
Bacteriophytochrome / Response regulator
Similarity search - Component
Biological speciesDeinococcus radiodurans R1 (radioresistant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWahlgren WY / Takala H / Westenhoff S
Funding supportEuropean Union, Finland, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)725642European Union
Academy of Finland330678 Finland
CitationJournal: Nat Commun / Year: 2022
Title: Structural mechanism of signal transduction in a phytochrome histidine kinase
Authors: Wahlgren WY / Claesson E / Tuure I / Trillo-Muyo S / Bodizs S / Ihalainen JA / Takala H / Westenhoff S
History
DepositionAug 27, 2022-
Header (metadata) releaseDec 21, 2022-
Map releaseDec 21, 2022-
UpdateDec 21, 2022-
Current statusDec 21, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15686.png

Downloads & links

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Map

FileDownload / File: emd_15686.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 448 pix.
= 386.042 Å		0.86 Å/pix.
x 448 pix.
= 386.042 Å		0.86 Å/pix.
x 448 pix.
= 386.042 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8617 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.6371145 - 1.0232408
Average (Standard dev.)-0.00032556194 (±0.0142761115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 386.0416 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_15686_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_15686_additional_1.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15686_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_15686_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

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Sample components

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Entire : Full-length bacteriophytochrome fused to its response regulator f...

EntireName: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
Components
  • Complex: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
    • Protein or peptide: Bacteriophytochrome,Response regulator
  • Ligand: BILIVERDINE IX ALPHA

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Supramolecule #1: Full-length bacteriophytochrome fused to its response regulator f...

SupramoleculeName: Full-length bacteriophytochrome fused to its response regulator from Deinococcus radiodurans.
type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Molecular weightTheoretical: 101 KDa

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Macromolecule #1: Bacteriophytochrome,Response regulator

MacromoleculeName: Bacteriophytochrome,Response regulator / type: protein_or_peptide / ID: 1
Details: Sample is a fusion of Deinococcus radiodurans DrBphP and its response regulator DrRR.,Sample is a fusion of Deinococcus radiodurans DrBphP and its response regulator DrRR.
Number of copies: 2 / Enantiomer: LEVO / EC number: histidine kinase
Source (natural)Organism: Deinococcus radiodurans R1 (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Molecular weightTheoretical: 101.579164 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MASMTGGQQM GRGSMSRDPL PFFPPLYLGG PEITTENCER EPIHIPGSIQ PHGALLTADG HSGEVLQMSL NAATFLGQEP TVLRGQTLA ALLPEQWPAL QAALPPGCPD ALQYRATLDW PAAGHLSLTV HRVGELLILE FEPTEAWDST GPHALRNAMF A LESAPNLR ...String:
MASMTGGQQM GRGSMSRDPL PFFPPLYLGG PEITTENCER EPIHIPGSIQ PHGALLTADG HSGEVLQMSL NAATFLGQEP TVLRGQTLA ALLPEQWPAL QAALPPGCPD ALQYRATLDW PAAGHLSLTV HRVGELLILE FEPTEAWDST GPHALRNAMF A LESAPNLR ALAEVATQTV RELTGFDRVM LYKFAPDATG EVIAEARREG LHAFLGHRFP ASDIPAQARA LYTRHLLRLT AD TRAAAVP LDPVLNPQTN APTPLGGAVL RATSPMHMQY LRNMGVGSSL SVSVVVGGQL WGLIACHHQT PYVLPPDLRT TLE YLGRLL SLQVQVKEAA DVAAFRQSLR EHHARVALAA AHSLSPHDTL SDPALDLLGL MRAGGLILRF EGRWQTLGEV PPAP AVDAL LAWLETQPGA LVQTDALGQL WPAGADLAPS AAGLLAISVG EGWSECLVWL RPELRLEVAW GGATPDQAKD DLGPR HSFD TYLEEKRGYA EPWHPGEIEE AQDLRDTLTG ALGERLSVIR DLNRALTQSN AEWRQYGFVI SHHMQEPVRL ISQFAE LLT RQPRAQDGSP DSPQTERITG FLLRETSRLR SLTQDLHTYT ALLSAPPPVR RPTPLGRVVD DVLQDLEPRI ADTGASI EV APELPVIAAD AGLLRDLLLH LIGNALTFGG PEPRIAVRTE RQGAGWSIAV SDQGAGIAPE YQERIFLLFQ RLGSLDEA L GNGLGLPLCR KIAELHGGTL TVESAPGEGS TFRCWLPDAG PLPGAADAAS SAGGSAGSAG MPERASVPLR LLLVEDNAA DIFLMEMALE YSSVHTELLV ARDGLEALEL LEQAKTGGPF PDLILLDLNM PRVDGFELLQ ALRADPHLAH LPAIVLTTSN DPSDVKRAY ALQANSYLTK PSTLEDFLQL IERLTAYWFG TAAIPQTYQP QLEHHHHHH

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Macromolecule #2: BILIVERDINE IX ALPHA

MacromoleculeName: BILIVERDINE IX ALPHA / type: ligand / ID: 2 / Number of copies: 2 / Formula: BLA
Molecular weightTheoretical: 582.646 Da
Chemical component information

ChemComp-BLA:
BILIVERDINE IX ALPHA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.3 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 98050
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4q0j


Chain - Chain ID: A
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8avx:
Cryo-EM structure of DrBphP in Pfr state

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